This file provides an overview of the types of figures that one can
potentially generate from each feature category to gain insight into the
features associating with disease conditions (Section 1).
Section 2 then runs an association study using the given features and
sample conditions and plots the key features from each feature category
using a representative figure.
The purpose is not to provide a comprehensive analysis in a single HTML but to help point directions for future investigation.
Here we provide a brief overview of the association study result, including the number of features in each feature type, and the number of features that are significantly associated ( P-value < 0.1) with the conditions of the interest.
knitr::include_graphics( system.file("extdata/figure", "celltypeproportion_example_figures.png", package = "scFeatures") )
## [1] "up regulated in Responder"
knitr::include_graphics( system.file("extdata/figure", "celltypegene_example_figures.png" , package = "scFeatures") )
## [1] "up regulated in Responder"
## [1] "up regulated"
knitr::include_graphics( system.file("extdata/figure", "pathway_example_figures.png" , package = "scFeatures") )
1. Heatmaps shows the top cell type specific pathway expression features
that differs between conditions
2. Boxplot shows the top cell type specific pathway expression features
that differs between conditions
3. PCA plot shows the separation of conditions based on the cell type
specific pathway expression features
## [1] "up regulated in Responder"
## [1] "up regulated in Responder"
knitr::include_graphics( system.file("extdata/figure",
"CCI_example_figures.png" , package = "scFeatures") )
1. Heatmap shows the top cell cell interactions features that differs
between conditions
2. Heatmap shows the difference in the number of interactions between
conditions
3. PCA plot shows the separation of conditions based on the cell type
specific pathway expression features
4. Network plot shows the difference in the number of interactions
between conditions 5. Boxplot shows the top cell cell interaction
features that differs between conditions
## [1] "up regulated in Responder"
## [1] "up regulated in Responder"
knitr::include_graphics( system.file("extdata/figure",
"aggregatedgene_example_figures.png" , package = "scFeatures") )
## [1] "up regulated in Responder"
## [1] "up regulated"
knitr::include_graphics( system.file("extdata/figure",
"spatial_example_figures.png", package = "scFeatures") )
## [1] "up regulated in WT"
## [1] "up regulated in WT"